Check the appropriate box below
if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions (see General Instruction A.2. below):

☐

Written communication pursuant to Rule 425 under the Securities Act (17 CFR 230.425)

Indicate by check mark whether the registrant is an emerging growth company as defined in Rule 405 of the Securities Act of 1933 (§230.405 of this
chapter) or Rule 12b-2 of the Securities Exchange Act of 1934 (§240.12b-2 of this chapter).

Emerging growth company ☐

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or
revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Item 7.01

Regulation FD Disclosure.

On September 8, 2017, Codexis, Inc. (the Company) updated
its corporate presentation (the Corporate Presentation) in connection with upcoming investor conferences. A copy of the Corporate Presentation is furnished as Exhibit 99.1 to this Current Report on Form 8-K, and incorporated by
reference herein.

The information furnished in this Current Report on Form 8-K pursuant to Item 7.01 (including Exhibit 99.1) shall not be deemed to
be filed under the Securities Exchange Act of 1934, as amended, nor shall it be incorporated into any future filing under the Securities Act of 1933, as amended, or under the Securities Exchange Act of 1934, as amended, unless the
Company expressly sets forth in such future filing that such information is to be considered filed or incorporated by reference therein.

Item 9.01

Financial Statements and Exhibits.

(d) Exhibits.

Exhibit

No.

Description

99.1

Corporate presentation of Codexis, Inc.

SIGNATURE

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned
hereunto duly authorized.

Forward-Looking Statements These slides and the accompanying oral presentation contain forward-looking
statements that involve risks and uncertainties. These statements relate to future events or our future financial or operational performance and involve known and unknown risks, uncertainties and other factors that could cause our actual results,
levels of activity, performance or achievement to differ materially from those expressed or implied by these forward-looking statements. Forward-looking statements include all statements that are not historical facts. In some cases, you can identify
forward-looking statements by terms such as ?may,? ?will,? ?should,? ?could,? ?would,? ?expects,? ?plans,? ?anticipates,? ?believes,? ?estimates,? ?projects,? ?predicts,? ?potential? or the negative of these terms, and similar expressions and
comparable terminology intended to identify forward-looking statements. These forward-looking statements represent our estimates and assumptions only as of the date hereof, and, except as required by law, we undertake no obligation to update or
revise publicly any forward-looking
statements, whether as a result of new information, future events or otherwise. Other factors that could materially affect actual results, levels of activity, performance or achievement can be found in Codexis?
Form 10-K for the period ended December 31, 2016 filed with the SEC on March 9, 2017 and Form 10-Q for the period ended June 30, 2017 filed with the SEC on August 9, 2017, including under the caption ?Risk Factors.? If any of these risks or
uncertainties materialize, or if our underlying assumptions prove to be incorrect, actual results, levels of activity, performance or achievement may vary significantly from what we projected. Our logo, ?Codexis,? ?CodeEvolver,? and other trademarks
or service marks of Codexis, Inc. appearing in this presentation are the property of Codexis, Inc. This presentation contains additional trade names, trademarks and service marks of other companies. We do not intend our use or display of other
companies? trade names, trademarks or service marks to imply relationships with, or endorsement or sponsorship of us by, these other companies. 2

CodeEvolver Licensing Creates Value Across Portfolio SOLUTION How to effectively leverage protein Licensed the
CodeEvolver platform engineering to improve GSK?s portfolio? Deeply embedded the technology in house Applications from discovery to post launch Codexis earns front end and back end economics Partnership created around shared vision for proteins and
mutual success of CodeEvolver ?We chose the Codexis platform after a thorough evaluation of the enzyme evolution landscape.? Doug Fuerst, GSK Technology Development Lead, Synthetic Biology 12